Project_Milestone_04

Author

Ngan Nguyen, Nicole Fernandez, Shirley Sui

Project Milestone #4: Visualizations

Submit an Rmd or Qmd and publish an html file on RPubs with the following:

Final datasets for creation of visualization

Join all datasets together
Calculate any remaining data elements needed for analysis
Show code used to create joined dataset, but please do not print full data frame output (showing data structure with str() is okay)

# Flu data only has quarters 2022.4 to 2023.2 Vax data has
# quarters 2022.1 to 2023.3 Before joining, filter vax data
# to only 2022.4 to 2023.2

df_vax <- df_vax %>%
    filter(quarter >= 2022.4 & quarter <= 2023.2)

# perform inner_join - we don't want any data that doesn't
# have a match in both datasets

df_joined <- inner_join(df_flu, df_vax, by = join_by(age_category,
    county, quarter)) %>%
    select(!c(sum_dx_new, sum_severe_new)) %>%
    drop_na()

# show data structure
str(df_joined)

tibble [678 × 6] (S3: tbl_df/tbl/data.frame)
 $ age_category         : chr [1:678] "0-17" "0-17" "0-17" "0-17" ...
 $ county               : chr [1:678] "Alameda County" "Alameda County" "Alameda County" "Amador County" ...
 $ quarter              : num [1:678] 2022 2023 2023 2022 2023 ...
 $ dx_new_rate          : num [1:678] 0.00493 0.03555 0.00671 0.00502 0.035 ...
 $ severe_new_rate      : num [1:678] 0.000751 0.000888 0.001812 0 0.001103 ...
 $ mean_vaccination_rate: num [1:678] 0.578 0.592 0.596 0.286 0.287 ...

Visualizations (at least one per group member)

One print quality table as requested in scenario
One print quality plot or chart as requested in scenario
For groups of 3, one additional print quality table or plot of your choice (can support the requested data in the scenario, or answer a different question using the same data sources)

Research Question(s)

CAUTION: It’s crucial to recognize that this analysis pertains to aggregate-level data, and caution should be exercised in generalizing these findings to individual-level dynamics to avoid the ecological fallacy.

Identify if COVID vaccination rates reflect flu vaccination rates in populations and or if more should be done to encourage flu vaccinations

# COVID vaccination rates vs flu rate (new cases), per
# quarter, color coded by county

# Re-format facet labels for quarters
qtr.labs <- c("Q4-2022", "Q1-2023", "Q2-2023")
names(qtr.labs) <- c(2022.4, 2023.1, 2023.2)

vax_flu_byqtr <- df_joined %>%
    group_by(county, quarter) %>%
    mutate(mean_vaccination_rate = mean(mean_vaccination_rate),
        dx_new_rate = mean(dx_new_rate)) %>%
    ggplot(aes(x = mean_vaccination_rate, y = dx_new_rate, color = county)) +
    geom_point() + geom_smooth(method = lm, color = "red") +
    theme_minimal() + scale_y_continuous(labels = function(x) round(x *
    100, digits = 2)) + labs(x = "Mean COVID Vaccination Rate 
  (fully vaccinated / population) ",
    y = "Mean Flu Rate 
  (new diagnoses / 100 susceptible)",
    title = "COVID vaccination rate does not significantly reflect flu vaccination rate",
    subtitle = "based on quarterly COVID vaccination rate data compared to simulated flu incidence rate data per 
quarter across 57 California counties, from Q4-2022 to Q2-2023") +
    facet_wrap(~quarter, scales = "free", labeller = labeller(quarter = qtr.labs)) +
    theme(legend.position = "none", plot.title.position = "plot",
        plot.title = element_text(face = "bold"), plot.subtitle = element_text(face = "italic"),
        strip.text.x = element_text(face = "bold"), axis.title.y = element_text(margin = margin(r = 5)),
        axis.title.x = element_text(margin = margin(t = 5)))

ggplotly(vax_flu_byqtr) %>%
    layout(title = list(text = paste0("COVID vaccination rate does not significantly reflect flu vaccination rate.",
        "<br>", "<sup>", "Across 57 California counties, from Q4-2022 to Q2-2023",
        "</sup>"), yref = "container", xref = "paper", yref = "paper"),
        annotations = list(text = paste0("<sup>", "Based on quarterly COVID vaccination rate data compared to simulated flu incidence rate data per quarter",
            "</sup>"), showarrow = F, xref = "paper", yref = "paper",
            xanchor = "right", yanchor = "auto", xshift = 350,
            yshift = -230), margin = list(t = 100, b = 110, l = 100,
            r = 30))

COVID vaccination rate vs flu rate interpretation: Analysis of the COVID vaccination rate data and simulated flu data indicates that COVID vaccination does not seem to strongly reflect flu vaccination within the 57 California counties from which data was collected/simulated. Additional measures to promote flu vaccination may be needed.

Identify where there is any correlation between COVID vaccination rates on flu rates and/or severity.

summary(df_joined)

 age_category          county             quarter      dx_new_rate      
 Length:678         Length:678         Min.   :2022   Min.   :0.003570  
 Class :character   Class :character   1st Qu.:2022   1st Qu.:0.004953  
 Mode  :character   Mode  :character   Median :2023   Median :0.006699  
                                       Mean   :2023   Mean   :0.015761  
                                       3rd Qu.:2023   3rd Qu.:0.035506  
                                       Max.   :2023   Max.   :0.040653  
 severe_new_rate    mean_vaccination_rate
 Min.   :0.000000   Min.   :0.1409       
 1st Qu.:0.002828   1st Qu.:0.4624       
 Median :0.015257   Median :0.7096       
 Mean   :0.038274   Mean   :0.6512       
 3rd Qu.:0.050552   3rd Qu.:0.8336       
 Max.   :0.428571   Max.   :1.1377

# Create categories based on COVID vaccination rates and
# severe flu rates
data <- df_joined %>%
    mutate(COVID_Vaccination_Rate = ifelse(mean_vaccination_rate <=
        median(mean_vaccination_rate), "Low Vaccination Rate (Min = 0.14)",
        "High Vaccination Rate (Max = 1.14)"), Severe_Flu_Rate = ifelse(severe_new_rate <=
        median(severe_new_rate), "Low Severe Flu Rate (Min = 0.00)",
        "High Severe Flu Rate (Max = 0.43)"))

# Calculate the correlation for each combination
correlation_table <- data %>%
    group_by(COVID_Vaccination_Rate, Severe_Flu_Rate) %>%
    summarise(Correlation = round(cor(mean_vaccination_rate,
        severe_new_rate), 2))

# Rename columns
colnames(correlation_table) <- c("COVID Vaccination Rate", "Mean Severe Flu Rate",
    "Correlation")

# Print the correlation table with kableExtra
kable(correlation_table, format = "html", caption = "No clear correlation between COVID vaccination rates and mean severe flu rate, Q4-2022 - Q2-2023") %>%
    kable_styling(full_width = FALSE)

No clear correlation between COVID vaccination rates and mean severe flu rate, Q4-2022 - Q2-2023
COVID Vaccination Rate	Mean Severe Flu Rate	Correlation
High Vaccination Rate (Max = 1.14)	High Severe Flu Rate (Max = 0.43)	0.10
High Vaccination Rate (Max = 1.14)	Low Severe Flu Rate (Min = 0.00)	-0.01
Low Vaccination Rate (Min = 0.14)	High Severe Flu Rate (Max = 0.43)	0.13
Low Vaccination Rate (Min = 0.14)	Low Severe Flu Rate (Min = 0.00)	0.45

Correlation table interpretation: Correlation values per each case provide insights into the relationships between COVID vaccination rates and severe flu cases rates in different scenarios, ranging from weak negative to moderate positive correlations. There is a significant weak negative correlation between the high vaccination rate group and low severe flu rate which might be impacted by confounders.

Does COVID vaccination affect flu severity within each age group?

# Visualization: One print quality plot or chart as
# requested in scenario Using Both a table & a chart seem
# appropriate for this specific research question Rename
# joined df
age_group_vax_vs_flu_severity <- df_joined

# Rename df
age_group_vax_vs_flu_severity_table <- age_group_vax_vs_flu_severity

# Create a summary table
summary_table <- age_group_vax_vs_flu_severity_table %>%
    group_by(age_category) %>%
    summarize(mean_vaccination_rate = mean(mean_vaccination_rate),
        mean_flu_severity = mean(severe_new_rate))

# Rename summary table data
colnames(summary_table) <- c("Age Category", "Mean COVID Vaccination Rate",
    "Mean Severe Flu Rate")

# Print the table using kableExtra (Quality table #1)
kable(summary_table, "html", caption = "High COVID vaccination rate does not necessarily imply low severe flu rate") %>%
    kable_styling(full_width = FALSE)

High COVID vaccination rate does not necessarily imply low severe flu rate
Age Category	Mean COVID Vaccination Rate	Mean Severe Flu Rate
0-17	0.3537977	0.0012448
18-49	0.6444651	0.0081145
50-64	0.7660298	0.0392774
65+	0.8302451	0.1031616

# Quality plot

# Scatter plot with facets for each age category
ggplot(data = age_group_vax_vs_flu_severity, aes(x = mean_vaccination_rate,
    y = severe_new_rate, color = mean_vaccination_rate)) + geom_point(size = 3) +
    labs(title = "High COVID vaccination rate does not necessarily imply low severe flu rate",
        subtitle = "Scatter Plots by Age Categories", x = "Mean Vaccination Rate",
        y = "Flu Severity Rate", color = "Mean Vaccination Rate") +
    geom_smooth(method = lm, color = "yellow") + scale_color_gradient(low = "blue",
    high = "red") + facet_wrap(~age_category, scales = "free") +
    theme_minimal()

COVID vaccination versus flu severity by age group interpretation: The data indicates an age-related uptrend in vaccination rates among the older demographics. Intriguingly, despite heightened vaccination coverage in these age groups, there is a simultaneous upswing in average flu severity.